Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-15 15:05:11 -0400 (Wed, 15 Sep 2021).

CHECK results for pogos on nebbiolo1

To the developers/maintainers of the pogos package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pogos.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1411/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pogos 1.12.2  (landing page)
VJ Carey
Snapshot Date: 2021-09-14 04:50:06 -0400 (Tue, 14 Sep 2021)
git_url: https://git.bioconductor.org/packages/pogos
git_branch: RELEASE_3_13
git_last_commit: 2735342
git_last_commit_date: 2021-08-29 09:34:59 -0400 (Sun, 29 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pogos
Version: 1.12.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pogos.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pogos_1.12.2.tar.gz
StartedAt: 2021-09-14 11:04:41 -0400 (Tue, 14 Sep 2021)
EndedAt: 2021-09-14 11:06:43 -0400 (Tue, 14 Sep 2021)
EllapsedTime: 122.2 seconds
RetCode: 0
Status:   OK  
CheckDir: pogos.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pogos.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pogos_1.12.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/pogos.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pogos/DESCRIPTION’ ... OK
* this is package ‘pogos’ version ‘1.12.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pogos’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compoundsByCell: no visible binding for global variable ‘cell_lines_v1’
compoundsByCell: no visible binding for global variable ‘compounds_v1’
compoundsByCell: no visible binding for global variable ‘datasets_v1’
lkc: no visible binding for global variable ‘cell_lines_v1’
lkc: no visible binding for global variable ‘compounds_v1’
lkc: no visible binding for global variable ‘datasets_v1’
plot,DRProfSet-missing: no visible binding for global variable ‘dose’
plot,DRProfSet-missing: no visible binding for global variable
  ‘response’
plot,DRProfSet-missing: no visible binding for global variable ‘drug’
plot,DRTraceSet-missing: no visible binding for global variable ‘dose’
plot,DRTraceSet-missing: no visible binding for global variable
  ‘response’
plot,DRTraceSet-missing: no visible binding for global variable
  ‘cell_line’
Undefined global functions or variables:
  cell_line cell_lines_v1 compounds_v1 datasets_v1 dose drug response
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/pogos.Rcheck/00check.log’
for details.



Installation output

pogos.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL pogos
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘pogos’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pogos)

Tests output

pogos.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(pogos)
Loading required package: rjson
Loading required package: httr
> 
> test_check("pogos")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  5.838   0.395   6.666 

Example timings

pogos.Rcheck/pogos-Ex.timings

nameusersystemelapsed
DRProfSet0.0020.0000.003
DRTraceSet0.7350.0041.817
basicDecoder0.0090.0000.061
compoundsByCell000
compounds_v10.0580.0040.062
iriCCLE0.2110.0320.243
rxdbQuery_v10.0120.0120.089
topEndpoints_v10.0000.0000.001
traces0.0080.0080.016